Lincoln Burrows (played by Dominic Purcell) is falsely and blatantly accused of the murder of Terrence Steadman and sentenced to death for the crime. He is surprised to see Michael Scofield in the same prison who plans to get him out of prison. He evaded authorities after escaping from prison and has been exonerated of all charges. Currently free, he has successfully assisted Michael and James Whistler to break out of Sona. As of season 4, he is now part of Self's covert "A-Team" assembled to bring down The Company. He is also in the very last scene when he visits Michael Scofield's (his brother) grave, and he puts an origami crane on top of the grave so he can remember the time when he made them for him, so he would always know that his brother was caring for him. In season 5, he finds out Michael is still alive and incarcerated in Yemen, and leads an operation to save his brother.

Michael Scofield (played by Wentworth Miller) is the protagonist of the series and younger brother of Lincoln Burrows. He designs an elaborate escape plan and tattoos it to his body to free his older brother who has been framed for murder and sentenced to death via the electric chair. He successfully executes this plan, freeing himself, Lincoln and 6 other convicts, but ultimately fails to evade the police in Panama. Season 3 is centered around Michael breaking out of prison again, however, this time from the self-governed prison of Sona, situated in Panama. In season 4, he reunites with Sara after discovering her death in season 3 was faked, and she is part of Agent Donald Self's covert "A-Team", which is assembled to bring down The Company. Michael has low latent inhibition, a personality trait which allows him to notice things that others would not. This, along with his genius-level intellect, is what enabled him to break out of both prisons. He also suffers from a tumor of the hypothalamus, which causes nosebleeds, disorientation, and extreme pain. In season 5, he is revealed to be incarcerated in Yemen under a different name.

Veronica Donovan (played by Robin Tunney) is a real-estate lawyer and a longtime friend of the protagonists of the series, who unsuccessfully tries to find evidence to exonerate Lincoln Burrows. She serves as the primary ally of the brothers in the show’s first season. Veronica had a relationship with Lincoln in High School and the two also dated each other after she graduated from Baylor law school. However, at the start of the show they have broken up since several years. When Lincoln is first framed for the murder of Terrence Steadman, Veronica assumes that he is guilty and moves on with her life. Sometime between the episode "Brother's Keeper", and the pilot, she gets engaged to Sebastian Balfour. Although she is a real estate lawyer and not a criminal lawyer, Veronica defends her childhood friend, Michael Scofield at his trial. Initially, she doesn't believe Lincoln's innocence and is convinced by the security tape footage. However, after the disappearance of Leticia Barris, a witness who could prove Lincoln's innocence and the death of a bishop who opposed Lincoln's death penalty, Veronica is led to believe that Lincoln might have been set up. Thus, Michael’s arrest causes her to grow more involved with Lincoln’s case, straining her relationship with Sebastian. Following the disappearance of Leticia in the episode "Cell Test", Veronica decides to postpone the wedding as she claims that she can’t focus on it at the time. Sebastian is hurt by this and breaks off the engagement.

She approaches Project Justice for help with Lincoln's case, knowing that she herself doesn't have any experience in death penalty cases. However, they refuse to partake in her case. Nick Savrinn later offers his help after telling her that his father was similarly accused of a crime he did not commit. Together, they work tirelessly, trying to uncover the truth behind Terrence Steadman's apparent murder. The original security tape which they were looking for is destroyed and in the subsequent episode, "Riots, Drills and the Devil Part 2", they are threatened via a public phone call in Washington, D.C. and are targeted by Paul Kellerman and Daniel Hale, who are members of the conspiracy. They were nearly killed by an explosion in Veronica's apartment and in the following episodes, LJ Burrows joins both of them after escaping from the agent's clutches. All three of them go into hiding. Their lives are once again in danger when an assassin called Agent Quinn manages to find out their secret location. Veronica eventually manages to knock him unconscious and escape with LJ and a wounded Nick. Veronica is then contacted by a secret informant, who claims to be willing to provide information. Knowing that hiding is not the answer, Veronica decides to go out into the open and reveal the conspiracy to the public. Veronica meets with the informant, agent Hale, the following night, where he reveals that Steadman is still alive. Hale is executed by Kellerman before he can provide proof, and Veronica barely has time to hide shortly before Kellerman arrives.

Now left more or less empty handed, Veronica and Nick nevertheless goes back to the court on Lincoln’s execution day for one last time to appeal for Lincoln’s case, but this ultimately fails as the judge rules against them. Fortunately, someone slips in evidence in the last minute which helps to stall Lincoln's execution. Veronica and Nick decide to send someone to do a test on Steadman's body, but the dental records matched Steadman's past records. Following this, she decides to find out where the real Steadman is hiding. In "J-Cat", Nick, Veronica and L.J. return to New Glarus to visit the dead Quinn, where they obtain his cell phone. Eventually, they found out Terrence Steadman's hideout in Blackfoot, Montana. However, at the end of the episode "Tonight", Veronica is betrayed by Nick, who turned out to have made a deal with John Abruzzi to have her "ready and waiting" at the airport on the night of the escape in exchange for his father’s freedom. Nick is conflicted, however, and ultimately lets her go to the airport as he doesn't want Veronica to be killed. Now alone, she travels to Blackfoot, Montana and manages to sneak into Steadman's house and confront him face to face.

In season 2, following her confrontation with Steadman (Jeff Perry), Veronica is executed in cold blood by secret service agents ordered to ensure that Terrence Steadman is kept hidden. Veronica becomes the first main character to be killed off in the series.

John Abruzzi (played by Peter Stormare) is an Italian-American mob boss and the Don of the Abruzzi crime family, who is imprisoned at Fox River with a life sentence. He controls Prison Industry, an internal work program for the convicts, thanks to his connections with Brad Bellick, who is on the payroll of Abruzzi's associates. He appears as an anti-hero where he is less of an antagonist than an unwanted ally to the protagonists. He is convicted based on the testimony of Otto Fibonacci, who saw him order the deaths of two men. Abruzzi plans to exact revenge on Fibonacci, who entered the witness protection program. In the pilot episode, he is approached by Michael Scofield with a PI membership request. Abruzzi at first dismisses the newcomer, but gives him his full attention after he learns that Michael somehow knows where Fibonacci is hiding. Although Michael claims that he will give up the information in exchange for help with his escape plan, Abruzzi has two of Michael's toes cut off trying to extract Fibonacci's location from him. This fails and Abruzzi decides to instead team up with Michael to break out of prison. Although their alliance is initially unstable, with both men being wary of each other, Abruzzi and Michael learn to get along as the season progresses. Abruzzi’s status as head of PI proves valuable to Michael’s escape plan, as the escape team is able to use work on PI to build an escape tunnel.

For some time, the escape plan is threatened when Abruzzi’s associate on the outside, Philly Falzone, cuts off Abruzzi's cash stream and takes his prison privileges from him as payback for failing to find Fibonacci. Together, Michael and Abruzzi decides to frame Falzone in the episode "Sleight of Hand", allowing Abruzzi to restore his control of PI. When fellow escapee T-Bag becomes an obstacle, Abruzzi has one of his men on the outside kidnap T-Bag's cousin. The job goes bad, resulting in the death of the cousin as well as his young son. Abruzzi is deeply shaken over the death of the toddler and turns to religion as an outlet for his pain, causing him to spare T-Bag’s life even though he had intended to kill him. This proves to be a big mistake, as T-Bag immediately takes the opportunity to slash Abruzzi's throat. He is evacuated by helicopter to receive treatment for his injuries. Abruzzi survives and returns six episodes later in "The Key". Upon his return he appears to have become very religious and friendly; it is soon discovered to be a ploy, as Abruzzi ruthlessly plans to kill most of the team and arranges to kidnap Veronica Donovan to force Fibonacci's location out of Michael, although this fails since Nick Savrinn released Veronica. After the escape, Abruzzi attempts to gun down T-Bag, but he handcuffs himself to Michael to avoid getting shot at. Abruzzi exacts revenge on T-Bag, cutting off his left hand with an axe, the one he attached himself to Michael with. He is one of the group of five who are forced to run on foot after his plane leaves them behind.

Abruzzi appears only briefly in season 2. After being on the run with the other four escapees, he separates from the group and reunites with his family in New York. No longer interested in finding out Fibonacci's location, he plans to flee with his family to Sardinia. He had a sudden change of mind when, one of his thugs informs him about Fibonacci's exact location, but is instead lured into a trap set up by Mahone and the FBI, using Fibonacci as bait. Rather choosing death over returning to prison, Abruzzi raises his weapon and is gunned down, with a cross in hand. He is the first member of the Fox River Eight to be taken down by the authorities.

In season 5, he is revealed to have an older son who did not appear in the original series, named Luca Abruzzi, who Lincoln began working for.

Production details

Peter Stormare, Abruzzi's portrayer, was a member of the regular cast and was featured in every episode before his character's injury in the thirteenth episode of the first season, "End of the Tunnel". After his return to the series six episodes later in "The Key", Stormare became a recurring guest star, appearing in the final four episodes of the first season and in the first, second and fourth episodes of the second season. The character was later killed off in the fourth episode of the second season, "First Down". He later appeared in a brief flashback in the episode "Fin Del Camino."

Fernando Sucre (played by Amaury Nolasco) is imprisoned at Fox River State Penitentiary for aggravated robbery and was ratted out by the man trying to steal his girlfriend. Sucre is Michael's cell mate and was one of the first members of the escape plan. Although the group split apart after the escape Sucre came back to help Michael multiple times. He is part of Self's "A-Team" and plays an important role in getting Scylla. In season 5, he is revealed to now be working on a freighter, and wants to help save Michael from Yemen.

Lincoln "L.J." Burrows Jr. (played by Marshall Allman) is Lincoln's estranged son. Marshall Allman was listed as part of the main cast until the fourteenth episode of the second season, "John Doe". In the pilot episode, despite his normally good behavior, L.J. is arrested for drug possession and put on probation. Part of his punishment is to visit a mentor, his father, once weekly. The first encounter is cold, but their relationship grows warmer, However, L.J. is targeted by conspiracy agents Paul Kellerman and Daniel Hale; after they frame him for the murders of his mother and stepfather, L. J. flees to Veronica Donovan and Nick Savrinn’s secret cabin. Upon discovering Kellerman's alias, he confronts him with a gun to avenge his mother. L.J. is arrested by the police after trying to shoot Kellerman. In season 2, L.J. is visited in jail by Alexander Mahone, who asks for his help to capture Lincoln and Michael; L.J. refuses to co-operate. His family nearly breaks him out of the courthouse, but the escape is foiled and L.J. is sent to an adult detention center. He is later set free in a move by The Company to find Lincoln. Though they are able to outsmart the agents and escape, they are arrested by the police in "Unearthed". They are later saved by people working for Lincoln's father, and L. J. is sent with his grandfather's friend Jane for safety.

In "Wash" L.J. is revealed to be living in Pullman, Washington under a false name. This ends in season 3, where L.J is kidnapped by The Company and held hostage as motivation for Lincoln and Michael to break Whistler out of Sona. After Whistler is broken out, the hostage exchange is successful at a museum, and L.J. is reunited with his father. L.J. appears briefly in the season 4 premiere and is briefly mentioned in the epilogue of the series finale when Lincoln says that L.J. is taking his finals in school, implying that wherever he is, he is doing well. L.J. does not appear in season 5, nor is he mentioned.

Brad Bellick (played by Wade Williams) is the leader of the Fox River State Penitentiary correctional officers but is later dismissed. He goes after Charles Westmoreland's hidden five million dollars, but fails. Set up for murder twice by T-Bag, he ended up incarcerated at Sona. He later escaped from Sona between Season's 3 and 4 along with Sucre and T-Bag. After his escape he was recruited to be part of Self's covert "A-Team" assembled to bring down The Company. He drowned while trying to put up a pipe to cross a main water conduit, saving the Scylla plan.

Paul Kellerman (played by Paul Adelstein) is a Secret Service agent who was ordered to make sure Lincoln Burrows is framed and convicted for murder, along with various other illegal acts. He was presumed dead after a shooting after releasing information about The Company at Sara Tancredi's trial at the end of season 2. He is revealed to still be alive at end of season 4.

In season 5, he is still working for the government, and is also revealed to be married and divorced with joint custody of a daughter.

Theodore "T-Bag" Bagwell (played by Robert Knepper) is imprisoned at Fox River State Penitentiary with a life sentence[1] for six accounts of kidnapping, rape, and murder. He escapes with Michael's help and reconnects with his previous family by kidnapping them. He frees them after an emotional outbreak, however. He goes to Panama and ends up in Sona for killing a number of prostitutes. T-Bag took over Sona after killing its former ruler, Lechero. However, sometime between season 3 and 4, he has broken out of Sona along with Sucre and Bellick and is now on a mission to head back to the US to settle the score with Michael for double-crossing him on the escape from Sona at the end of season 3. He later is forced to be a reluctant member of Self's "A-Team". In season 5, he is released from Fox River and given an operation which gives him a prosthetic hand as functional as a natural one. he is also given a photo which shows Michael is still alive in Yemen, and becomes an unwanted ally of Sara. Though Bagwell initially believed himself to be incapable of fathering a child due to being conceived as a result of inbreeding, Michael reveals to him that he has an illegitimate son in David "Whip" Martin. The chance for a fresh start and family serves as T-Bag's motivation for continuing to assist Michael. When Whip is killed, T-Bag snaps the neck of his killer; and as a result finds himself imprisoned in Fox River; where he exacts further vengeance upon Poseidon, who is assigned his cellmate.

Sara Tancredi (played by Sarah Wayne Callies) is Michael's love interest, daughter of the Illinois governor, and a doctor working at Fox River State Penitentiary before becoming involved in the conspiracy behind Lincoln Burrows' setup. She eventually shoots a corrupt government agent, William Kim, and Michael takes the fall for it, giving her freedom. Apparently brutally decapitated, her head was placed in the box at the beginning of season 3, though it was later discovered to be a ploy and she is in fact alive. As of season 4, she was part of Self's covert "A-Team" assembled to bring down The Company. In season 5, she has remarried, is raising Michael's son alongside her husband, and is somewhat reluctant to believe Michael is still alive.

Benjamin Miles "C-Note" Franklin (played by Rockmond Dunbar) is imprisoned at Fox River for possession of stolen goods.[2] He escapes prison and reconnects successfully with his family. All charges against him are dropped after he reveals certain secrets about Alexander Mahone. He and his family are safe and were then put in witness protection at the end of season 2. C-Note returns at the end of season 4 with Sucre to help Michael, Lincoln & the rest of the team against The Company. In season 5, he accompanies Lincoln to Yemen after finding evidence that Michael is still alive.

Alexander Mahone (played by William Fichtner) is an FBI Special Agent, who is put in charge of the nationwide manhunt for the Fox River escapees. He is responsible for the deaths of three of the Fox River Eight. In turn, Michael sets him up for possession of cocaine, which leads to his incarceration at Sona, as well. He escaped from Sona with Michael and Whistler at the end of season 3, and is now part of Self's covert "A-Team" assembled to bring down The Company in season 4. He does not appear in Season 5, nor is he mentioned.

Little is known about his background, though throughout season three James Whistler (played by Chris Vance) repeatedly claimed to be a simple fisherman from Kalbarri in Western Australia who ran charters between Panama and the Pacific North West.[3]

He is in the Panamanian jail known as Sona for the murder of the son of the mayor of Panama City during a bar fight, although he claims he is innocent. This resulted in a bounty being placed on his head, as the mayor offered to free (via a corrupt judge) any inmate who would kill Whistler, forcing Whistler to go into hiding in the sewers after he arrived at the prison.[4] His only contact with the outside world was his girlfriend Sofía, who obliviously believes in his innocence. Breaking him out of Sona became Michael Scofield's primary mission during season three, though Whistler and his mysterious background causes tension between both men as various aspects of Whistler's background (most notably the story that he is needed to be freed in order to deliver vaguely explained "coordinates" recorded within a bird watcher guidebook Whistler carries with him at all times) cause Michael to question whether or not he is helping an innocent man caught in the vast web of conspiracies of The Company, as Whistler claims to be.

He is first seen in Orientación hiding within a crawlspace below the room of Lechero, the de facto leader of the prison. When he first saw Brad Bellick, he offered him food in return for a favor. When a fight broke out between two inmates (one of whom was Michael Scofield) Bellick was to place a note on each of the two inmates in order to get more food from Whistler. He was apparently attempting to send a message to Sofia Lugo. Sofía found the note, which read "VERSAILLES 1989 V MADRID", and lead her to a bank lock-box containing what appeared to be a bird guide. The book was then stolen by Lincoln Burrows.

The Company seems to have an interest in Whistler, and this is apparently the reason Michael's incarceration in Sona was arranged in the first place. Due to the political spotlight on him, The Company were unable to get him out. Initially, Whistler is seemingly unaware of why The Company wants him. One of The Company's operatives, Elliott Pike, approached Michael and offered their support if he breaks Whistler out. When he refused, another operative, who called herself only by the obviously false name Susan B. Anthony, approached Michael's brother Lincoln Burrows and informed them that Lincoln's son L.J. Burrows and Michael's girlfriend Sara Tancredi were being held hostage by The Company and would be killed if Michael didn't break Whistler out within a week.

After the bounty on his head and his location is discovered by both Michael and Mahone, Mahone delivers him to prison boss Lechero. Fortunately, Lechero chooses to remove the bounty on Whistler at Michael's request, giving up the reward of freedom from the mayor, after Michael restores water to the prison. Whistler tries to befriend Mahone in an effort to get information on Scofield. Later he reveals why The Company is interested in him. They want to know where Whistler took a certain naturalist to during one of his charters. But he needs the bird guide, which is actually his trip log to retrace his steps and take The Company to that location.

In Good Fences the bird guide is returned to him with the warning that he is running out of time. Meanwhile, he asks Sofía to look into Scofield and Burrows because he doesn't trust any of them. Also he tells Sofía The Company is interested in him because of a charter he did in Seattle. Michael instructs Whistler to spy on one of the tower guards to learn their behavior. Whistler observes a window of 6 minutes where the sun's glare forces the guard to look away. When it is revealed he covers for Michael by claiming to be a bird lover. Meanwhile, a new inmate, Tyge claims to know him, calling him by the name McFadden and seeing him in 1997 in Nice at the Ambassadorhotel, thus casting doubt on his story in Michael's eyes.

Tyge is murdered and Whistler is suspected after McGrady tips off Lechero that the two had an argument. His life is in danger until Michael manages to intervene. In Vamonos it is later revealed that Whistler has been deceitful with Michael, and has actually been working with Gretchen (Susan B. Anthony), and that it is he who is orchestrating his break from Sona. Susan aka Gretchen tells him the plan Bang and Burn is in effect, which both dismissed as suicide until Pad Man says it is the only option after Michael failed to take James out of Sona. While James gets to the roof of Sona during a military helicopter rescue of him, Michael Scofield, knowing his position is dead without him, stops the prison break. Scofield was then taken away to confess what he knew about the helicopter squad.

Scofield's confession caused Whistler to be implicated. In the subsequent torture, Whistler revealed Gretchen Morgan, the woman who had been orchestrating the entire escape. After learning that Gretchen escaped from the Sona guards clutches, both Whistler and Scofield returned to Sona. Whistler, Michael, Mahone, and McGrady later escape from Sona, Lechero is shot and injured, while T-Bag and Bellick are caught during the escape. He realizes he lost his book during his escape. After getting out of Sona, Whistler manages to escape from Michael and Lincoln but is then caught again. The exchange for L.J. and him goes well, but it is realized there never were coordinates in the bird book. He tries to explain to Sofía, but at this point she wants nothing to do with him. He escapes with Gretchen and The Company. He is later seen making a deal with Mahone to join up with The Company and Mahone, Gretchen, and he drives away.

Whistler appears briefly in the season 4 premiere. After he betrays The Company by planning to steal Scylla, he is shot and killed by Company hitman Wyatt. A later episode reveals that he had arranged to sell Scylla to the Chinese, rather than handing it over to the government.

Norman St. John (played by Robert Wisdom) is a Panamanian drug kingpin incarcerated at Sona, where he is the leader of the prison and is at the top of the prison hierarchy. He appears only in season 3 where his role is similar of that of John Abruzzi in season 1. Ruthless and violent, he earned the nickname "Lechero" when he, at the age of 13, disguised himself as a lechero (milkman) in order to kill his mother's rapist. The character serves as an antagonist and enemy to the protagonists in the early episodes of season 3, but later becomes an uneasy ally. Lechero is introduced in the season 3 premiere episode Orientacion. Aware of Michael Scofield's ventures as a fugitive from the United States, Lechero views him as a threat to his rule and plots to get rid of him by setting Michael up in a fight to the death with another prisoner. However, Michael survives. Lechero also meets T-Bag in this episode and accepts him as his underling. The relationship between him and Michael continues to be characterized by deceit and mistrust in the next few episodes, like in Call Waiting, when Michael steals Lechero’s cell phone. But Lechero learns in Fire/Water, that Michael can be useful as well when he restores water to the prison. Lechero grows increasingly paranoid as the season progresses, and is later tricked by T-Bag that his cronies are planning a coup against him, successfully manipulating Lechero to enlist T-Bag as a spy.

In Good Fences, Lechero gets in trouble when the electrical system in the prison stops functioning. Remembering that Michael is an engineer, he quickly enlists Michael's help to fix the system, in exchange for a new cell in the prison block. He is later approached by Bellick, who warns him that Michael cannot be trusted and that he will trick Lechero as he tricked Bellick. At first Lechero is skeptical but then he decides to see for himself, and when Michael successfully outwits him and repairs the prison's electrical system, his trust in Michael is solidified. He later punishes Bellick for the bad information by scalding him with hot coffee. In Photo Finish Lechero slits Cheo for taking tribute from Augusto (It was actually Sammy). In Vamonos after Michael's failed escape, Lechero informs him that he will break out of prison, but with one catch—he must take Lechero with him. In the following episode Bang & Burn, Lechero reveals an underground tunnel which they can use to escape. in the episode Hell or High Water Lechero is shot by the guards during the Sona Escape. In the following episode The Art of the Deal T-Bag and Bellick come to Lechero's aid. T-Bag tells Lechero that the guards will let them go for 50,000 dollars. Lechero calls his girlfriend who brings T-Bag the money. After getting the money T-Bag takes his place as the leader of Sona by suffocating Lechero with a pillow while Bellick stands by and watches in terror.

Sofía Lugo (played by Danay García) is the girlfriend of James Whistler. Having worked with Lincoln to help Michael break out Whistler in Season 3, she is with LJ in Season 4, though their whereabouts are unknown. The character is introduced to the series as a regular in the premiere episode of the third season of the series. Sofía Lugo is first seen posing as the wife of a dead inmate and a gravedigger, in order to get James Whistler's message written to her, transferred via the dead bodies. Sofía finds the note, which refers to a bank lock-box in a bank where a bird guide is contained. The book is then stolen by Lincoln Burrows and tells her to tell Whistler that he has it now. She meets Whistler in Sona, who keeps her in the dark about Scofield as he feared that Sofía might be killed if she knew too much. On her way out, she sees the visitation log, figures the connection and notes Lincoln's hotel and room number. She tails Lincoln to Saint Rita and confronts him. Lincoln tells her about the escape plan.

In "Good Fences", Sofía meets Whistler who demands to know the truth. He relents, telling her of The Company's interest in him and telling her to gather information on the brothers. Afterwards she meets Lincoln at his hotel wanting to help in the escape. Lincoln enlists her as an impromptu translator for Lincoln and the grave digger. Sofía helps to bargain with the price of the car of the grave digger, who is killed shortly after by Gretchen. She also accompanies Lincoln to bury the scuba gear and provides assistance, such as helping to drug one of the guards and hatching the escape plan for Scofield and James Whistler. She seemed to not completely trust Lincoln but in "Bang & Burn", she discovers Whistler's other identity and house, which casts doubt into her mind. A romantic connection begins to appear between Lincoln and Sofía due to her problems of mistrust with her boyfriend James Whistler. Later, in an attempt to force Whistler to give the coordinates, Sofía is captured and tortured by Gretchen Morgan.

In the season finale, after the exchange, Sofía decided to break up with Whistler, when she realized that she could no longer trust him. Sofía was shot by one of The Company members in "The Art of the Deal", but has not yet given in to the extent of her injuries. As she recovers in the hospital, she tells Michael to retrieve a box from her apartment which she had found, containing files on a man named Jason Lief. As Michael leaves to find Whistler, Lincoln and LJ decided to stay back to take care of Sofía.

Sofía appears briefly in the premiere episode of season 4, shopping with Lincoln and LJ, but when Lincoln kills a Company agent and is arrested, Sofía and L.J. run for it.

She reappears in the finale of season 4. She is held captive by Company agents but is released unharmed by the General after Sucre and C-Note apprehend him. Four years later, she is shown to be romantically involved with Lincoln.

Sofia does not appear in season 5, but in "Progeny" Lincoln mentions that he and Sofia have broken up.

Gretchen Louise Morgan (played by Jodi Lyn O'Keefe), sometimes operating under the alias Susan B. Anthony, is introduced to the series in the third season as a high-ranking Company field-operative in charge of Whistler's breakout from Sona. Despite claiming to have killed Sara, season 4 revealed she lied and Sara is in fact alive. Gretchen finds herself in The Company's crosshairs after the Whistler/Scylla disaster and later is forced out of necessity to aid Self's "A-Team" against her former employers. She is ruthless and impatient, performing swift executions without hesitation if there is any obstacle to her plan, but is known to have a soft side for the few individuals that she cares about, for example her daughter. She is shown to be able to withstand torture and is exceptionally skilled in martial arts. Her character is mainly an antagonist, and later an occasional, uneasy ally to the protagonists. Gretchen is the main antagonist of the third season. The character is first seen covering scratch wounds on her face with makeup. Later, she meets up with Lincoln at a bar and informs him that The Company has kidnapped both Sara and LJ, and that in order for them to survive, Michael must break James Whistler out of Sona prison. When Lincoln tries to rescue both of them, she claimed to have personally beheaded Sara and warned the brothers not to play games.[5] Gretchen provides assistance to both of the brothers so that their plan would work, such as money for the gravedigger (whom she eventually executed as she suspected that he might report them to the police)[5] and a drug that could help silence a guard.[6] When she finds out that Lincoln is trying to drug the guard much earlier than the hostage exchange time, she becomes furious and moves to behead the fearful LJ,[6] but is stopped when Lincoln reveals the truth. When the escape ultimately fails, Gretchen's supervisor, General Krantz, forced her to carry out the "Bang and Burn" Operation, which involved flying helicopters into Sona to retrieve Whistler. Due to Michael's intervention, this operation fails. Hoping that Lincoln could once again be included into the plan, Gretchen allowed Lincoln to meet his son at an abandoned shack. Michael's confession caused her to be subsequently tortured by waterboarding by Sona guards. However, Gretchen was able to escape from their clutches.[7]James Whistler later revealed that her real name is Gretchen Morgan.[8] Following Michael and Whistler's escape from Sona, Gretchen was able to extract Whistler safely, but she failed to eliminate the brothers. In her final appearance of the season, she is seen driving away in a car with Whistler and Mahone (who had seemingly made a deal with Whistler to work for The Company after the escape).

In the season 4 premiere, Gretchen appears with Whistler on a mission to retrieve one of the Scylla cards, which fails when Whistler betrays The Company by stealing the original card, and Gretchen is punished by the general for her failure. Initially assumed dead, she is revealed to be alive at the end of "Breaking and Entering", locked away and tortured for information. She has only a minimal role in the next few episodes, but finally escapes custody in the fifth episode. "Blow Out" fleshes out her character when Gretchen takes shelter at her sister’s house. It is revealed that Rita’s child Emily is actually Gretchen’s daughter, and the character shows her first hints of a softer side when they appear in scenes together. Following this, Gretchen recovers and enters the main plot to obtain Scylla. She tracks down T-Bag, who is in possession of Whistler’s bird book, and forces him to co-operate. She eventually becomes a reluctant ally to Michael and his team, which includes Sara. In an effort to make amends with Sara, whom Gretchen tortured in Panama, she meets with her in "The Price" and offers her to get even by whipping Gretchen with a bull whip. Sara declines, instead stating that Gretchen will one day pay for the guard she murdered that helped Sara escape. In "Greatness Achieved", Gretchen is revealed to be a former lover of the General (who is also the father of her daughter, Emily) when she infiltrates his office with a gun seeking revenge. While she appears to soften at his manipulations, it is later revealed that she is merely playing along to gain inside information.

Gretchen and T-Bag serve mainly as wild cards in these episodes, playing Michael’s team, with their real plan revealed to be using them to get Scylla, only to then steal it and sell it to a Chinese crime syndicate for 125 million. In their scenes together, Gretchen is often the more ruthless character, while T-Bag appears more hesitant as he grows attached to salesman Cole Pfeiffer, the alias he is living under to facilitate the break-in. In order to speed things along, Gretchen accepts the task of trying to steal the general's Scylla card by seducing him in "Quite Riot". He uncovers her true motivation, however, and she barely survives by pleading with him, confirming to the viewers that he is the father of her child. On the day of the break-in to steal Scylla, Gretchen and T-Bag stake out the Gate corporation with machine guns, preparing to ambush the team when they return. Gretchen and a reluctant T-Bag take the entire company hostage when someone spots her gun, and they are forced to flee when a federal agent arrives. In the next few episodes, Gretchen shares a plotline with Don Self, a Homeland Security agent that Michael’s team reports to. After betraying the team and taking Scylla, Self threatens the life of Gretchen’s daughter for her to help him find a new buyer. Gretchen complies and in "Going Under" they meet with the buyer, but fails when men appear to take them into Company custody. Following this, she is forced by the general to work with Self, Lincoln and T-Bag to recover Scylla. Her character is later written out when she is shot by the buyer and the rest of the team leave her behind to be arrested by the police.

In The Final Break, Gretchen is shown to be an inmate in the prison that Sara is taken to, for the murder of Christina Scofield Hampton. When Gretchen sees Lincoln and Sucre standing outside the prison, she demands that Sara take her along in any escape plan they may be developing. While initially threatening, Gretchen eventually reveals to Sara that she simply desires to see her daughter, Emily, and to give her a necklace which she made herself. She proves her loyalty by saving Sara from an attacker looking to collect a bounty put out by the General, who is incarcerated in a neighboring prison. When the escape commences, Gretchen attacks a guard and gets stabbed in the leg. Knowing that she cannot escape without help, Gretchen asks Sara to choose to either leave her behind or help her, and Sara lends her hand. Finally, as Sara and Gretchen are on their way, Gretchen is spotted by guards. When asked whether or not she is alone, Gretchen refuses to reveal Sara's presence, and gets taken back into custody. This is the last time she is seen. Before leaving however, Sara sees the necklace Gretchen made for her daughter on the ground, and, knowing she would have been caught had Gretchen betrayed her, Sara secures it, so that she may pass it along to Emily.

Donald "Don" Self (played by Michael Rapaport) is an ICE Homeland Security Investigations (DHS) special agent introduced in the fourth-season premiere. After their arrest, he recruits the protagonists and several other characters into a covert "A-Team" of sorts in a mission to take down The Company once and for all. The character plays a prominent role in the last season. Not much is known about him but he is stated as a hardworking Homeland Security Agent who tries to bring down The Company but has yet to be successful. He has worked for five years to bring down The Company with James Whistler and Aldo Burrows (Michael and Lincoln's father), the latter has also tried to locate Scylla. According to a background check made on the character by The Company in the episode "Five the Hard Way", Self studied law on Long Island, before spending the next 18 years moving around DOD and DOJ. He began working for Homeland Security in 2002. Agent Self later told Mahone that he had a wife that died while giving birth - his unborn infant died too. A picture of his wife is seen at his desk several times and he once played a message of her voice at his answering machine.[9][10] The truth about his wife's fate is revealed near the end of the season. Self's character plays the role of supervisor and ally to the team in the first half of the season, but later becomes an antagonist. In "Scylla", he tasks Lincoln Burrows and Michael Scofield with the mission of bringing down The Company and finding "Scylla", a key card that stores a wealth of information about The Company. He promises them full exoneration if the brothers can obtain Scylla and hand it over to the government. As Sucre, Mahone, Bellick, Sara, and Roland Glenn, a computer hijacker, come along with them, Self points out that if they do it there is no coming back and that he is their boss.[9][11] The partnership with Self is not without friction, however. Most notably in "Shut Down" were Self, under pressure from his boss, reluctantly tries to cancel the mission after it is discovered that Scylla is six key cards, not just one. Self agrees to let them find the rest of the Scylla cards after the team successfully identifies the other cardholders.[12] In other episodes throughout the season, however, the character provides active assistance to the team, like in "Safe and Sound" where Self, although overtly pessimistic about their chances, agree to help by first contriving an excuse to enter a cardholder’s office and later in the episode by luring someone out of his office for lunch, leaving the team to get to a safe which contains a Scylla card.[13] He also has his computer analysts identify the rest of the cardholders from the picture taken with Michael's cell phone.

When General Krantz, the leader of The Company, discovers Self had images of him enhanced, Wyatt confronts Self and tells him that the General "likes his privacy."[14] Taking Mahone's advice; to get aggressive, Self meets the General face-to-face and blackmails him, threatening to reveal to the public missions he was involved in, thus making it harder for The Company to remain covert.[15] As the season unfolds, Self's character begins to show tendencies of a more ruthless side. He often threatens to kill those who oppose him, and in "Blow Out", after Mahone becomes a liability to the mission by getting arrested by the police, Self wants to have Mahone killed, something Michael refuses to do. Instead the team rescue Mahone, without Self’s assistance. In "The Legend" the team grows a dislike for Self when he seems unwilling to hold up his end of the deal and send Bellick’s body home after he died in the previous episode. However, in "Quiet Riot", he is actively supportive of the mission and seems to genuinely want to bring down The Company. Self's character shows his true colours in the episode "Selfless," where he apparently works with the team as they finally manage to recover the Scylla, but ultimately betrays both them and his government superiors by stealing the recovered Scylla and keeping it for himself. His real character motivation is revealed to be finding a 'buyer' for Scylla, an apparently private interest. Realizing that the needs to find a new buyer after the first one is killed, Self murders his partner, federal agent Miriam Holtz, in cold blood in order to get to T-Bag, a prisoner she was guarding. From this point onwards, the character begins to share a more active role in the plot by being out in the field and appearing in more action-oriented scenes. In the next few episodes, he is an antagonist to Michael and the rest of the team. After faking his death and attempting to frame Michael's team for it in "Deal or No Deal", Self uses T-Bag to track down the family of Gretchen Morgan, a former Company operative that has gone rogue. Self threatens the life of her daughter to gain her co-operation and the two characters share the same plotline for the next few episodes, as they use Gretchen's contacts to find another buyer for Scylla. However, at the end of the episode, Self finds himself with a problem: the mistrust of Michael Scofield, who removed a part of the Scylla device. While his apprehension of T-Bag led to Gretchen and a buyer, he cannot sell Scylla while it is incomplete. Thus, the episode ends with him ultimately demanding the missing part of Scylla from Michael, who instead suggests he "Come and get it".

In the next episode, "Just Business" Self seemingly makes a deal with Michael to sell Scylla together, while both parties are actually plotting against each other. Self and Gretchen plants an x-ray device in the warehouse to try to find the missing piece of scylla while the team are planning to take the rest of Scylla back from Self. In the end it is Self who is successful, as he and Gretchen obtains the missing piece and head out to meet Gretchen’s contact, a conduit named Vikan. Self’s character is again shown to be ruthless when, after asking Vikan if the buyer of Scylla is coming, Self shoots Vikan and his bodyguards and tosses their corpse into the sea so that he doesn’t have to share a cut of the money with them. Self is next seen waiting with Gretchen for the Scylla buyer. After getting a call from Gretchen's sister, Rita, Gretchen tells Self that The Company has T-Bag and unfortunately he might have told The Company where they are. So before Lincoln and Sucre could track them, Self and Gretchen destroy their cell phones and flee. They're next seen at a phone store and look injured with bloody scratches on their faces. They buy a new phone and tell the store owner not to tell anyone they were there. They head to the warehouse to wait for the buyer. The buyer arrives and Self and Gretchen hold the buyer at gunpoint. Gretchen forces Self to hand Scylla to the buyer or they will be in grave danger. Self hands over Scylla. They hear noise and Self and Gretchen go to investigate, but are betrayed by the buyer when he points his gun at them and they run for cover and a shootout occurs. The buyer shoots Self in the shoulder and flees with the money and Scylla. Later they are to work with Lincoln and T-Bag to recover Scylla. Self’s character plays a less prominent role in the season’s final episodes, where he works with his new team to find Scylla and track down the new buyer, which turns out to be Lincoln and Michael’s mother, Christina Rose Scofield. When the team fails in their assignment, the general decides to punish them by ordering the death of one of their family members and singles out Self's wife, who is actually alive and in a persistent vegetative state due to Self's drunk and reckless behavior. Self then escapes, but gets arrested when at the hospital, where one of Christina's men injects him with a serum that gradually leaves him in the same state his wife was in. He refuses to help federal agents with locating Burrows and Scofield because they failed at protecting him, and is left in his vegetative state for the rest of his life. In his final appearance in the epilogue of the Series Finale, set four years after the events of the rest of the episode, Self is revealed to be living at a rest facility, using a wheelchair, mute and drooling.

Jacob Anton Ness (played by Mark Feuerstein) is an economics professor at University of Syracuse, and Sara's second husband and Mike's stepfather. He and Sara were married sometime during the seven years after Michael's supposed death. In the season premiere, he is shot in the leg by someone supposedly sent to kill Sara and Mike due to Lincoln investigating Michael's death, and spends the next two episodes recovering in the hospital. During this time, Sara finds out Michael is still alive under the name Kaniel Outis, and tells him. He tells her that Michael may have succumbed to madness due to the choices he made. After being released, he, Sara and Mike lie low at his parents' lake house per Sara's choice, though he says the university has resources that can be used to find their attackers. T-Bag eventually tracks the attackers to a meeting with him. Sara confronts him on this, and he claims he was paying them off to leave him alone, and later seems to prove this by having them arrested with a tracker in the money, forgiving Sara for her paranoia. However, Michael later reveals him to be "Poseidon", a rogue CIA agent that he has been working for in exchange for exoneration of himself and others. Michael also reveals that he murdered the CIA agent Michael's alias is accused of having murdered. Sara returns to New York and tries to pretend she does not know, but he sees through this immediately, and captures her and Mike. Michael, Lincoln and their contacts try to catch him, and manage to track him to his lake house, but he seemingly turns the tables and has one of his subordinates ambush Michael and Mike, with Sara's fate unknown. He is ultimately caught and incarcerated at Fox River, where he is attacked by T-Bag as retribution for Whip's death.

Sheba (played by Inbar Lavi) is a woman who leads a resistance movement in Yemen, and C-Note's contact when he and Lincoln arrive. She allows the two to visit Ogygia, and later helps them rescue a man who can help them facilitate Michael's escape, as well as his daughter and several schoolgirls, from ISIL. She and Lincoln later attempt to get fake passports, but are captured, and she is nearly raped by a one-eyed man who had a crush on her in high school, but is saved by Lincoln. She and C-Note bring the people they saved from ISIL to an airport and manage to get on board a small plane, but are forced to leave without Michael, Lincoln and their fellow escapees. They make it to Jordan, and eventually back to the States, where she and C-Note regroup with Michael and Lincoln, and help them track down Poseidon and his subordinates to find Sara and Mike. Eventually, when Michael figures out where they are, Lincoln kisses her and sends her back to take care of the others, claiming he could not forgive himself if something happened to her.

David "Whip" Martin (played by Augustus Prew) is first introduced as Michael's cellmate in Ogygia in season 5. He is quickly revealed to know that Michael is not Kaniel Outis, and that he and Michael have been breaking people out of prisons around the world for years. Michael repeatedly calls him his (Michael's) whip-hand, hence his nickname. He is loyal to Michael despite not knowing his real name, but as their time in Ogygia goes on and their escape plan doesn't seem to be working, he starts to become more paranoid that Michael will betray him, which only increases when Abu Ramal, the prisoner they are in Ogygia to break out, is released from solitary confinement. Michael repeatedly tells him he will not leave him, but he continues to be frightened, even fighting Michael and forcing a guard to break them up (though this is part of Michael's plan). He confronts Michael during the escape, where Michael finally reveals his plan to leave Ramal behind, satisfying Whip. However, the escape fails, and he, Michael, Ramal and their cellmate Ja are thrown into solitary confinement, where he starts to become paranoid once again as ISIL strikes land closer to the prison. After Michael convinces Ramal to help them escape, he and Ja are released from their cells when Michael gets the keys. They try to persuade Michael to leave Ramal behind, but Michael admits he is necessary. Eventually the four escape the prison along with Sid, another inmate, and formulate a plan to double-cross Ramal, but he turns the tables on them. Whip tells Ramal he was arrested for killing a man in a barfight, and when they are surprised by Lincoln, he takes the opportunity to kill Ramal, which ends up backfiring. With ISIL hunting them, he continues to follow Michael, now knowing his real name, despite two of their plans for escape failing. Eventually the group tries to escape across the desert to Phaecia, a small fishing village, and Whip kills several ISIL members following them. He accompanies Michael and Lincoln to Crete, Greece, and expresses his admiration for an injured Michael. He then accompanies them on to a freighter, arranged by Sucre, back to the States. When they are caught by NAVY Seals, he escapes with Michael, Lincoln and Sucre in a life raft, and is taken by fishing boat to France, from where Michael instead sends him to Chicago instead of New York. During this time, it is revealed that his real name is David Martin, and that he was a survivor in prison, which is why Michael chose him as his partner (and the cover story he told Ramal may have been why he was originally incarcerated). In Chicago, he follows coordinates given by Michael to Lake Michigan, where he meets T-Bag. T-Bag reveals that he is in fact his father, which is the reason why he Michael made him his whip-hand.